| Chain sequence(s) |
A: MSEMEKIEEEIKRLIKELEELMERLKELVEAGGPLVLVARKMEEIKELVEKLKRLLEELGTRGVTAACSHARKSSGLPEELFEEAKRAIEKAEKLIKEVEASLTPEEKERIKKILKENEEIEKELRAILAADRTGVSASCSHNGESGPFDLARRLIEMLEKRLEEFEKKLEEEKKKKLEEAKNKGVTAACPHAGAKGFDLKKVEEFKKELEEEKKKMLSELLLSIALTIDRLARQETDPAVRRDLRLVLIYVLAEALRERKEEVEKLTKQFKAVLAERLKALEEEATKGVTAACSHNGKSGQVKDAELEREIKRVELLLRNPDITVHVIIVALEVGVEEALLLLKDPQAMVDTLLAMPLERIIEHLELILETARLRPELLDAAELERLIAEFRALA
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:19:34)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/e3d24797402932a/tmp/folded.pdb (00:19:34)
[INFO] Main: Simulation completed successfully. (00:25:19)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 1 | M | A | -0.9813 | |
| 2 | S | A | -1.6027 | |
| 3 | E | A | -2.8305 | |
| 4 | M | A | -2.2496 | |
| 5 | E | A | -2.9187 | |
| 6 | K | A | -3.5469 | |
| 7 | I | A | -2.5399 | |
| 8 | E | A | -2.6825 | |
| 9 | E | A | -3.8971 | |
| 10 | E | A | -2.8482 | |
| 11 | I | A | 0.0000 | |
| 12 | K | A | -3.6078 | |
| 13 | R | A | -3.2683 | |
| 14 | L | A | 0.0000 | |
| 15 | I | A | -2.6703 | |
| 16 | K | A | -3.1842 | |
| 17 | E | A | -2.4644 | |
| 18 | L | A | 0.0000 | |
| 19 | E | A | -2.3723 | |
| 20 | E | A | -2.9545 | |
| 21 | L | A | -1.9953 | |
| 22 | M | A | 0.0000 | |
| 23 | E | A | -3.2097 | |
| 24 | R | A | -2.4696 | |
| 25 | L | A | 0.0000 | |
| 26 | K | A | -2.4863 | |
| 27 | E | A | -2.6288 | |
| 28 | L | A | 0.0000 | |
| 29 | V | A | -0.8652 | |
| 30 | E | A | -2.2412 | |
| 31 | A | A | -1.5216 | |
| 32 | G | A | -1.0859 | |
| 33 | G | A | -0.6604 | |
| 34 | P | A | 0.0000 | |
| 35 | L | A | 0.0560 | |
| 36 | V | A | 0.0000 | |
| 37 | L | A | 0.0000 | |
| 38 | V | A | 0.0000 | |
| 39 | A | A | 0.0000 | |
| 40 | R | A | 0.0000 | |
| 41 | K | A | 0.0000 | |
| 42 | M | A | -1.5249 | |
| 43 | E | A | -2.5613 | |
| 44 | E | A | -1.9209 | |
| 45 | I | A | 0.0000 | |
| 46 | K | A | -2.8667 | |
| 47 | E | A | -2.9146 | |
| 48 | L | A | -1.8427 | |
| 49 | V | A | 0.0000 | |
| 50 | E | A | -2.6416 | |
| 51 | K | A | -2.3218 | |
| 52 | L | A | 0.0000 | |
| 53 | K | A | -2.4288 | |
| 54 | R | A | -2.4611 | |
| 55 | L | A | -1.6164 | |
| 56 | L | A | 0.0000 | |
| 57 | E | A | -2.8287 | |
| 58 | E | A | -1.9909 | |
| 59 | L | A | 0.0000 | |
| 60 | G | A | -0.9502 | |
| 61 | T | A | -0.5298 | |
| 62 | R | A | -0.5368 | |
| 63 | G | A | -0.0849 | |
| 64 | V | A | 1.5672 | |
| 65 | T | A | 0.7106 | |
| 66 | A | A | 0.1241 | |
| 67 | A | A | 0.0402 | |
| 68 | C | A | 0.6242 | |
| 69 | S | A | -0.7330 | |
| 70 | H | A | -1.4193 | |
| 71 | A | A | -1.9190 | |
| 72 | R | A | -2.9506 | |
| 73 | K | A | -2.9987 | |
| 74 | S | A | -1.5627 | |
| 75 | S | A | -1.1702 | |
| 76 | G | A | -1.1932 | |
| 77 | L | A | -1.6183 | |
| 78 | P | A | -2.0277 | |
| 79 | E | A | -3.5060 | |
| 80 | E | A | -3.3523 | |
| 81 | L | A | -2.4270 | |
| 82 | F | A | -2.2279 | |
| 83 | E | A | -3.7420 | |
| 84 | E | A | -4.1031 | |
| 85 | A | A | 0.0000 | |
| 86 | K | A | -3.2626 | |
| 87 | R | A | -4.1460 | |
| 88 | A | A | 0.0000 | |
| 89 | I | A | -3.1244 | |
| 90 | E | A | -3.9515 | |
| 91 | K | A | -3.0901 | |
| 92 | A | A | 0.0000 | |
| 93 | E | A | -3.4394 | |
| 94 | K | A | -3.8011 | |
| 95 | L | A | 0.0000 | |
| 96 | I | A | 0.0000 | |
| 97 | K | A | -3.9431 | |
| 98 | E | A | -3.6353 | |
| 99 | V | A | -2.2279 | |
| 100 | E | A | -2.8801 | |
| 101 | A | A | -1.9640 | |
| 102 | S | A | -1.3409 | |
| 103 | L | A | -1.1837 | |
| 104 | T | A | -1.3850 | |
| 105 | P | A | -1.8810 | |
| 106 | E | A | -3.0512 | |
| 107 | E | A | -2.3752 | |
| 108 | K | A | -2.8696 | |
| 109 | E | A | -3.5016 | |
| 110 | R | A | -2.7356 | |
| 111 | I | A | 0.0000 | |
| 112 | K | A | -3.1146 | |
| 113 | K | A | -2.3339 | |
| 114 | I | A | 0.0000 | |
| 115 | L | A | -2.0923 | |
| 116 | K | A | -3.0939 | |
| 117 | E | A | 0.0000 | |
| 118 | N | A | 0.0000 | |
| 119 | E | A | -3.5469 | |
| 120 | E | A | -3.3788 | |
| 121 | I | A | 0.0000 | |
| 122 | E | A | -2.4475 | |
| 123 | K | A | -3.0930 | |
| 124 | E | A | -2.0174 | |
| 125 | L | A | 0.0000 | |
| 126 | R | A | -1.4558 | |
| 127 | A | A | -1.0567 | |
| 128 | I | A | -0.4645 | |
| 129 | L | A | 0.0000 | |
| 130 | A | A | -0.5814 | |
| 131 | A | A | -0.2018 | |
| 132 | D | A | -0.9819 | |
| 133 | R | A | -1.4558 | |
| 134 | T | A | -0.6155 | |
| 135 | G | A | -0.3392 | |
| 136 | V | A | 1.0285 | |
| 137 | S | A | 0.2831 | |
| 138 | A | A | 0.1096 | |
| 139 | S | A | 0.2005 | |
| 140 | C | A | 0.0427 | |
| 141 | S | A | -0.9117 | |
| 142 | H | A | -1.6358 | |
| 143 | N | A | -2.4186 | |
| 144 | G | A | -2.4639 | |
| 145 | E | A | -2.5254 | |
| 146 | S | A | -1.6452 | |
| 147 | G | A | -1.1194 | |
| 148 | P | A | -0.8674 | |
| 149 | F | A | -0.8020 | |
| 150 | D | A | -1.2947 | |
| 151 | L | A | 0.0000 | |
| 152 | A | A | 0.0000 | |
| 153 | R | A | -1.5129 | |
| 154 | R | A | -1.3948 | |
| 155 | L | A | 0.0000 | |
| 156 | I | A | 0.0000 | |
| 157 | E | A | -1.7114 | |
| 158 | M | A | -1.2963 | |
| 159 | L | A | 0.0000 | |
| 160 | E | A | -1.9010 | |
| 161 | K | A | -2.7855 | |
| 162 | R | A | -2.4577 | |
| 163 | L | A | 0.0000 | |
| 164 | E | A | -4.0574 | |
| 165 | E | A | -4.1259 | |
| 166 | F | A | 0.0000 | |
| 167 | E | A | -3.9232 | |
| 168 | K | A | -4.3278 | |
| 169 | K | A | -3.7051 | |
| 170 | L | A | 0.0000 | |
| 171 | E | A | -3.4615 | |
| 172 | E | A | -4.0004 | |
| 173 | E | A | -3.3396 | |
| 174 | K | A | -3.4696 | |
| 175 | K | A | -3.6326 | |
| 176 | K | A | -4.2770 | |
| 177 | K | A | -3.3541 | |
| 178 | L | A | -3.2213 | |
| 179 | E | A | -4.5974 | |
| 180 | E | A | -4.3851 | |
| 181 | A | A | -3.0440 | |
| 182 | K | A | -2.6469 | |
| 183 | N | A | -3.0281 | |
| 184 | K | A | -2.8189 | |
| 185 | G | A | -1.2431 | |
| 186 | V | A | 0.5223 | |
| 187 | T | A | -0.1448 | |
| 188 | A | A | 0.2352 | |
| 189 | A | A | 0.2672 | |
| 190 | C | A | 0.4240 | |
| 191 | P | A | -0.4558 | |
| 192 | H | A | -0.9831 | |
| 193 | A | A | -0.8557 | |
| 194 | G | A | -1.1635 | |
| 195 | A | A | -1.1196 | |
| 196 | K | A | -1.8795 | |
| 197 | G | A | -0.7501 | |
| 198 | F | A | 0.2753 | |
| 199 | D | A | -1.2225 | |
| 200 | L | A | -0.4422 | |
| 201 | K | A | -2.6524 | |
| 202 | K | A | -2.7298 | |
| 203 | V | A | -2.1591 | |
| 204 | E | A | -3.4339 | |
| 205 | E | A | -2.9389 | |
| 206 | F | A | -2.5501 | |
| 207 | K | A | -3.5215 | |
| 208 | K | A | -3.7382 | |
| 209 | E | A | -3.6270 | |
| 210 | L | A | 0.0000 | |
| 211 | E | A | -3.6669 | |
| 212 | E | A | -4.1125 | |
| 213 | E | A | -3.2082 | |
| 214 | K | A | 0.0000 | |
| 215 | K | A | -3.3874 | |
| 216 | K | A | -2.7251 | |
| 217 | M | A | 0.0000 | |
| 218 | L | A | -1.4927 | |
| 219 | S | A | 0.0000 | |
| 220 | E | A | 0.0000 | |
| 221 | L | A | 0.0000 | |
| 222 | L | A | 0.0000 | |
| 223 | L | A | 0.0000 | |
| 224 | S | A | 0.0000 | |
| 225 | I | A | 0.0000 | |
| 226 | A | A | 0.0000 | |
| 227 | L | A | 0.0000 | |
| 228 | T | A | 0.0000 | |
| 229 | I | A | 0.0000 | |
| 230 | D | A | 0.0000 | |
| 231 | R | A | -1.4976 | |
| 232 | L | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | R | A | -2.4965 | |
| 235 | Q | A | -2.3608 | |
| 236 | E | A | -1.6840 | |
| 237 | T | A | -1.1470 | |
| 238 | D | A | -1.2031 | |
| 239 | P | A | -0.9218 | |
| 240 | A | A | -0.6509 | |
| 241 | V | A | -0.9274 | |
| 242 | R | A | -1.5633 | |
| 243 | R | A | -1.1091 | |
| 244 | D | A | -0.9242 | |
| 245 | L | A | 0.0000 | |
| 246 | R | A | -0.7054 | |
| 247 | L | A | 0.0000 | |
| 248 | V | A | 0.0000 | |
| 249 | L | A | 0.0000 | |
| 250 | I | A | 0.0000 | |
| 251 | Y | A | 0.0000 | |
| 252 | V | A | 0.0000 | |
| 253 | L | A | 0.0000 | |
| 254 | A | A | 0.0000 | |
| 255 | E | A | 0.0000 | |
| 256 | A | A | 0.0000 | |
| 257 | L | A | 0.0000 | |
| 258 | R | A | -2.0830 | |
| 259 | E | A | -2.5633 | |
| 260 | R | A | -2.6976 | |
| 261 | K | A | -3.1819 | |
| 262 | E | A | -3.6970 | |
| 263 | E | A | -2.4714 | |
| 264 | V | A | 0.0000 | |
| 265 | E | A | -3.4193 | |
| 266 | K | A | -3.2044 | |
| 267 | L | A | 0.0000 | |
| 268 | T | A | 0.0000 | |
| 269 | K | A | -3.0286 | |
| 270 | Q | A | -2.3185 | |
| 271 | F | A | 0.0000 | |
| 272 | K | A | -1.4077 | |
| 273 | A | A | -1.2819 | |
| 274 | V | A | 0.0000 | |
| 275 | L | A | 0.0000 | |
| 276 | A | A | -1.4110 | |
| 277 | E | A | -2.7113 | |
| 278 | R | A | -2.0581 | |
| 279 | L | A | -2.2764 | |
| 280 | K | A | -3.6647 | |
| 281 | A | A | -2.8878 | |
| 282 | L | A | 0.0000 | |
| 283 | E | A | -4.4082 | |
| 284 | E | A | -4.3985 | |
| 285 | E | A | -4.0251 | |
| 286 | A | A | -2.8601 | |
| 287 | T | A | -2.0893 | |
| 288 | K | A | -2.5742 | |
| 289 | G | A | -1.2479 | |
| 290 | V | A | 0.6653 | |
| 291 | T | A | 0.0638 | |
| 292 | A | A | -0.6530 | |
| 293 | A | A | 0.0000 | |
| 294 | C | A | -0.0420 | |
| 295 | S | A | -0.4112 | |
| 296 | H | A | -1.8944 | |
| 297 | N | A | -2.5458 | |
| 298 | G | A | -1.6639 | |
| 299 | K | A | -2.4507 | |
| 300 | S | A | -1.5429 | |
| 301 | G | A | 0.0000 | |
| 302 | Q | A | -1.2183 | |
| 303 | V | A | -0.3152 | |
| 304 | K | A | -2.0729 | |
| 305 | D | A | -2.1595 | |
| 306 | A | A | -2.1310 | |
| 307 | E | A | -2.9167 | |
| 308 | L | A | -2.8329 | |
| 309 | E | A | -3.3542 | |
| 310 | R | A | -2.9004 | |
| 311 | E | A | -1.8715 | |
| 312 | I | A | -1.6955 | |
| 313 | K | A | -1.4135 | |
| 314 | R | A | 0.0000 | |
| 315 | V | A | 0.0000 | |
| 316 | E | A | -0.9848 | |
| 317 | L | A | 0.0000 | |
| 318 | L | A | 0.0000 | |
| 319 | L | A | -0.4771 | |
| 320 | R | A | -1.1753 | |
| 321 | N | A | 0.0000 | |
| 322 | P | A | -0.7273 | |
| 323 | D | A | -1.0556 | |
| 324 | I | A | 0.0000 | |
| 325 | T | A | -0.5941 | |
| 326 | V | A | 0.0000 | |
| 327 | H | A | 0.0000 | |
| 328 | V | A | 0.0000 | |
| 329 | I | A | 0.0000 | |
| 330 | I | A | 0.0000 | |
| 331 | V | A | 0.0000 | |
| 332 | A | A | 0.0000 | |
| 333 | L | A | 0.0000 | |
| 334 | E | A | 0.1204 | |
| 335 | V | A | 0.9772 | |
| 336 | G | A | 0.0000 | |
| 337 | V | A | 0.0000 | |
| 338 | E | A | -0.2062 | |
| 339 | E | A | -0.2029 | |
| 340 | A | A | 0.0000 | |
| 341 | L | A | 0.0000 | |
| 342 | L | A | -0.5946 | |
| 343 | L | A | -0.5001 | |
| 344 | L | A | 0.0000 | |
| 345 | K | A | -1.0644 | |
| 346 | D | A | -1.4418 | |
| 347 | P | A | 0.0000 | |
| 348 | Q | A | -1.2955 | |
| 349 | A | A | -0.7667 | |
| 350 | M | A | 0.0000 | |
| 351 | V | A | 0.0000 | |
| 352 | D | A | -0.7837 | |
| 353 | T | A | -0.2513 | |
| 354 | L | A | 0.0000 | |
| 355 | L | A | 0.0000 | |
| 356 | A | A | -0.1739 | |
| 357 | M | A | 0.0000 | |
| 358 | P | A | -1.0182 | |
| 359 | L | A | -1.4783 | |
| 360 | E | A | -2.5964 | |
| 361 | R | A | -1.9210 | |
| 362 | I | A | 0.0000 | |
| 363 | I | A | -1.6159 | |
| 364 | E | A | -1.7595 | |
| 365 | H | A | 0.0000 | |
| 366 | L | A | 0.0000 | |
| 367 | E | A | -0.9088 | |
| 368 | L | A | 0.0000 | |
| 369 | I | A | 0.0000 | |
| 370 | L | A | 0.0000 | |
| 371 | E | A | -0.9628 | |
| 372 | T | A | 0.0000 | |
| 373 | A | A | 0.0000 | |
| 374 | R | A | -2.3418 | |
| 375 | L | A | -1.1652 | |
| 376 | R | A | -1.6874 | |
| 377 | P | A | -2.1333 | |
| 378 | E | A | -2.4012 | |
| 379 | L | A | -1.2773 | |
| 380 | L | A | -1.4796 | |
| 381 | D | A | -2.5923 | |
| 382 | A | A | -1.8467 | |
| 383 | A | A | -1.1475 | |
| 384 | E | A | -1.4828 | |
| 385 | L | A | 0.0000 | |
| 386 | E | A | -1.8240 | |
| 387 | R | A | -1.6627 | |
| 388 | L | A | 0.0000 | |
| 389 | I | A | 0.0000 | |
| 390 | A | A | -1.2542 | |
| 391 | E | A | -1.1758 | |
| 392 | F | A | 0.0000 | |
| 393 | R | A | -2.1764 | |
| 394 | A | A | -0.8748 | |
| 395 | L | A | 0.0000 | |
| 396 | A | A | -0.9004 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.
pH |
Average A4D Score |
Max A4D Score |
|||
| 4.0 | -1.3987 | 2.3839 | View | CSV | PDB |
| 4.5 | -1.5223 | 2.3867 | View | CSV | PDB |
| 5.0 | -1.6857 | 2.3952 | View | CSV | PDB |
| 5.5 | -1.8545 | 2.4185 | View | CSV | PDB |
| 6.0 | -1.9856 | 2.4706 | View | CSV | PDB |
| 6.5 | -2.0447 | 2.5519 | View | CSV | PDB |
| 7.0 | -2.026 | 2.6328 | View | CSV | PDB |
| 7.5 | -1.9516 | 2.6842 | View | CSV | PDB |
| 8.0 | -1.8486 | 2.7071 | View | CSV | PDB |
| 8.5 | -1.7326 | 2.7154 | View | CSV | PDB |
| 9.0 | -1.6102 | 2.7767 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine